TY  - JOUR
AU  - Hoopes, Genevieve
AU  - Meng, Xiaoxi
AU  - Hamilton, John P.
AU  - Achakkagari, Sai Reddy
AU  - de Alves Freitas Guesdes, Fernanda
AU  - Bolger, Marie E.
AU  - Coombs, Joseph J.
AU  - Esselink, Danny
AU  - Kaiser, Natalie R.
AU  - Kodde, Linda
AU  - Kyriakidou, Maria
AU  - Lavrijssen, Brian
AU  - van Lieshout, Natascha
AU  - Shereda, Rachel
AU  - Tuttle, Heather K.
AU  - Vaillancourt, Brieanne
AU  - Wood, Joshua C.
AU  - de Boer, Jan M.
AU  - Bornowski, Nolan
AU  - Bourke, Peter
AU  - Douches, David
AU  - van Eck, Herman J.
AU  - Ellis, Dave
AU  - Feldman, Max J.
AU  - Gardner, Kyle M.
AU  - Hopman, Johannes C. P.
AU  - Jiang, Jiming
AU  - De Jong, Walter S.
AU  - Kuhl, Joseph C.
AU  - Novy, Richard G.
AU  - Oome, Stan
AU  - Sathuvalli, Vidyasagar
AU  - Tan, Ek Han
AU  - Ursum, Remco A.
AU  - Vales, M. Isabel
AU  - Vining, Kelly
AU  - Visser, Richard G. F.
AU  - Vossen, Jack
AU  - Yencho, G. Craig
AU  - Anglin, Noelle L.
AU  - Bachem, Christian W. B.
AU  - Endelman, Jeffrey B.
AU  - Shannon, Laura M.
AU  - Strömvik, Martina V.
AU  - Tai, Helen H.
AU  - Usadel, Björn
AU  - Buell, C. Robin
AU  - Finkers, Richard
TI  - Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
JO  - Molecular plant
VL  - 15
IS  - 3
SN  - 1674-2052
CY  - Oxford
PB  - Oxford Univ. Press
M1  - FZJ-2022-01120
SP  - 520-536
PY  - 2022
AB  - Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder’s efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.
LB  - PUB:(DE-HGF)16
C6  - pmid:35026436
UR  - <Go to ISI:>//WOS:000767562700006
DO  - DOI:10.1016/j.molp.2022.01.003
UR  - https://juser.fz-juelich.de/record/905938
ER  -